People are very careful (and rightfully so) to say when they don't understand the words of the Achronim or Rishonim to not say they are/were "wrong". But rather to say "I don't understand what he means". Perhaps as well to be careful not to say "it doesn't make sense". I've seen at times the Achronim and Rishonim were also careful to write this way. However do we ever find that perhaps they wrote a later more "sharply" and did say "this doesn't make sense" or that "he is/was wrong"? At any point in history.

"Not the Raavad"? There are lots of instances in which the Raavad accuses the Rambam of having made things up, and uses very harsh language to do so.
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Shimon bMApr 3 '13 at 12:32

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There are literally dozens of them, and I see them all the time. Nothing comes immediately to mind, but flicking through the beginning of Yesodei haTorah, I see a hasagah on 6:4 that commences with "זה אינו כלום".
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Shimon bMApr 3 '13 at 13:00

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The terms "ולא היא" ("it is not so") and "תמיה" (or some variant, meaning, roughly, "unbelievable") come up quite frequently, although this is often followed by "לפע״ד" ("in my humble opinion").

For one example, the ב"ח in יורה דעה צ"ד levies several criticisms at many others among both his contemporaries and his predecessors, using לפע״ד at least once in the midst of the criticisms, and ends with "כנלפע"ד" ("so it seems to my humble opinion"), although the "end" doesn't close without a couple more direct rejections of both the positions of the שלחן ערוך and the רמ"א.

There are numerous examples of rishonim expressly calling people out for speaking falsely, and while the number of people to do so diminishes with time (unless they're speaking about their own contemporaries), it nonetheless remains a phenomenon. The Maharshal, for example (Rabbi Shlomo Luria), believed that anybody is capable of disputing with anybody else, so long as he spends the time to actually learn all of the primary material. (My source for that is a published PhD dissertation by Edward Fram, as quoted on the Wikipedia entry for Maharshal.)

Consider also the Gra's commentary on Yoreh Deah 179:6 (Biur haGra, §179.13). There, he says that the Rambam was led astray by his own philosophy (והפילוסופיא הטתו) to say things that are patently untrue.

I wish the Maharshal would be more easy to find inside (where ever this Edward Fram might be getting it from.)
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YehoshuaApr 3 '13 at 12:57

I don't know if Fram is getting this from his Yam shel Shlomo or his Chokhmat Shlomo. I don't have access to the former and as for the latter, I see nothing in his introduction that would suggest that. I am going to assume that, by virtue of this being a PhD, Fram did actually learn the works of the Maharshal, and is basing his statement on actual passages therein. But I would have to see his thesis to know for certain.
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Shimon bMApr 3 '13 at 13:06

Rabbi Ovadia Yosef has on several occaisions said that a certain Acharon or even Rishon was wrong. He does so respectfully, usually saying, "and with all due respect to
his honor, this is not so." You can find at least one instance quoted in this review of one of the several biographies on Rav Ovadia Yosef. (see page 7 right hand column five lines from the bottom).

There is also the Arabanel who wrote an entire book(Rosh Amanah) rejecting the Rambam's thirteen principles. As does the Hatam Sofer(see Rabbi March Shapiro's book The Limits of Orthodox Theology: Rambam's Thirteen Principles Reprised).

Maran Rav Ovadia was always upset that people wrote in Seforim that the Rishonim are wrong. What you should do? You should work hard to explain where the Rishon is coming from! He did however Pasken with chosing whichever Rishon is more accepted.

Regarding Achronim see introduction to Eigeret Leben Torah by Rav Yitzcak Yosef it saids there that בעצם there is no problem but since the generation changed its better to refrain from using such words.

One interesting example saying directly and explicitly that earlier authorities where wrong is in regards to Rambam's opinion that a woman's seven niddah days and eleven zavah days strictly alternate and various other aspects of his approach to niddah and zavah.

You can also take a look at Rav Slifkin's monograph, The Sun's Path at Night, which documents that many Rishonim openly said that Chazal erred in certain scientific matters, and documents that the approach of reinterpreting these matters as having mystical meaning is a very late occurrence.